1 / 14

Modeling Biomolecules Using the WWW

Modeling Biomolecules Using the WWW. Major Classes of Biomolecules. Peptides (Proteins) Carbohydrates Nucleic Acids Lipids. Modeling Peptides. Primary structure

palmer-hale
Télécharger la présentation

Modeling Biomolecules Using the WWW

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. Modeling Biomolecules Using the WWW

  2. Major Classes of Biomolecules • Peptides (Proteins) • Carbohydrates • Nucleic Acids • Lipids

  3. Modeling Peptides • Primary structure • Most molecular modeling software allows construction of peptide models by appending pre-constructed amino acids in sequence, usually by selecting their 1- or 3-letter abbreviations. • Secondary structure • features such as a-helix, b (pleated) sheet, hairpin turns, etc. can be specified (examples on following panel).

  4. Alpha Helix Secondary Structure

  5. Beta Sheet Secondary Structure

  6. Hairpin Turn Secondary Structure Hairpin turn, alpha helix Hairpin turn, Beta sheet

  7. Modeling Peptides... • Tertiary structure • folding of chains…more difficult to model accurately, unless structure is known from X-ray or NMR. • Quaternary structure • Combination of several subunits...likewise difficult to model accurately, unless structure is known from X-ray or NMR.

  8. Modeling Peptides... • Computations are usually limited to molecular mechanics, although semi-empirical MO calculations can be performed on small biopolymers. • MM Forcefields designed for biomolecules: • Amber (peptides and nucleic acids)/Kollman • OPLS (peptides and nucleic acids)/Jorgensen • BIO+ (biomacromolecules)/Karplus (all of these are found in HyperChem)

  9. Modeling Biomolecules using HyperChem

  10. HyperChem • Special database for Peptides • 20 Pre-optimized amino acids • Peptide menu choices • a helix • b (pleated) sheet • other • Termination modes: • NH2 or NH3+; CO2H or CO2-

  11. Spartan • Special database for Nucleotides • 4 Pre-optimized bases (A,T,C,G) • Nucleotide menu choices • DNA (double strand), DNA (single strand) • RNA (double strand), RNA (single strand) • DNA-RNA mixed • A, B or Z helical forms (differ in rise/base)

  12. WWW pages dealing with Modeling Biomolecules • Georgia State University molecular modeling site: modeling problems, biomolecules: http://heme.gsu.edu/glactone/ • Dr. Barry Honig’s web site (Columbia University… great images of biomolecules):http://wiki.c2b2.columbia.edu/honiglab_public/index.php/Main_Page

  13. WWW pages dealing with Modeling Biomolecules... • Molecular Graphics (rendering); University of Geneva, Switzerland (Dr. Jacques Weber) http://scsg9.unige.ch/fln/eng/toc.html • NIH Center for Molecular Modelinghttp://cmm.info.nih.gov/modeling/

  14. WWW pages dealing with Modeling Biomolecules... • Molecular Modeling Research Group at the Dept. of Agricultural Environmental Sciences and Food Biotechnology, University of Sassari - ITALY:http://antas.agraria.uniss.it • The Research Collaboratory for Structural Bioinformatics (PDB database of structures of proteins and other biomolecules):http://www.rcsb.org

More Related